[cybmole]

actually, - thinking about this some more - you don't need to do that 2nd conversion at all. i just add original version of book to calibre, change cover art, then use calibre to send book to device. When calibre sends it back to kindle it should automatically add in the new art work

but if that fails / or you want to debug - then read on....

the 5 way navigation on kindle looks for things called header tags in the code.

I cannot think of anything in calibre processing that would remove those, so
describe in riduculous detail exactly how you "I go in and alter the metadata (change the cover art) and then do another conversion"
& maybe that will help.
it must be something in your "another conversion" settings

check how do things look & work after you have edited metadata but before the 2nd conversion

try also - on the screen called mobi conversion there is an option to force generate TOC - see what happens if you tick that box when doing the 2nd conversion

as you are new to this i recommen bypass understanding structure detection for now. this seems to be a case of the structure beign ok to begin with, but something is getting lost / over-written in mobi to mobi conversion.

actually, - thinking about this some more. you done have to do that 2nd conversion at all. it should be suffiicent to just add book to calibre, change cover art, send book to device. when calibre sends it back to kindle it should automatically add in the new art work